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root/OpenMD/trunk/src/applications/dynamicProps/DynamicProps.cpp
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Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 321 by tim, Sun Feb 13 07:25:22 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <iostream>
# Line 49 | Line 49
49   #include "utils/simError.h"
50  
51   #include "applications/dynamicProps/DynamicPropsCmd.h"
52 < #include "applications/dynamicProps/DCorrFunc.hpp"
52 > #include "applications/dynamicProps/DipoleCorrFunc.hpp"
53   #include "applications/dynamicProps/RCorrFunc.hpp"
54   #include "applications/dynamicProps/VCorrFunc.hpp"
55 + #include "applications/dynamicProps/LegendreCorrFunc.hpp"
56 + #include "applications/dynamicProps/RadialRCorrFunc.hpp"
57 + #include "applications/dynamicProps/ThetaCorrFunc.hpp"
58 + #include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
59 + #include "applications/dynamicProps/EnergyCorrFunc.hpp"
60  
56 – using namespace oopse;
61  
62 + using namespace OpenMD;
63 +
64   int main(int argc, char* argv[]){
65    
66 <    //register force fields
67 <    registerForceFields();
66 >  //register force fields
67 >  registerForceFields();
68  
69 <    gengetopt_args_info args_info;
69 >  gengetopt_args_info args_info;
70  
71 <    //parse the command line option
72 <    if (cmdline_parser (argc, argv, &args_info) != 0) {
73 <        exit(1) ;
74 <    }
71 >  //parse the command line option
72 >  if (cmdline_parser (argc, argv, &args_info) != 0) {
73 >    exit(1) ;
74 >  }
75  
76  
77 <    //get the dumpfile name and meta-data file name
78 <    std::string dumpFileName = args_info.input_arg;
73 <
74 <    std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
75 <
77 >  //get the dumpfile name and meta-data file name
78 >  std::string dumpFileName = args_info.input_arg;
79      
80 <    std::string sele1;
81 <    std::string sele2;
80 >  std::string sele1;
81 >  std::string sele2;
82  
83 <    if (args_info.sele1_given) {
84 <        sele1 = args_info.sele1_arg;
83 >  if (args_info.sele1_given) {
84 >    sele1 = args_info.sele1_arg;
85 >  }else {
86 >    char*  sele1Env= getenv("SELECTION1");
87 >    if (sele1Env) {
88 >      sele1 = sele1Env;
89      }else {
90 <        char*  sele1Env= getenv("OOPSE_SELE1");
91 <        if (sele1Env) {
92 <            sele1 = sele1Env;
93 <        }else {
94 <            sprintf( painCave.errMsg,
88 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
89 <            painCave.severity = OOPSE_ERROR;
90 <            painCave.isFatal = 1;
91 <            simError();
92 <        }
90 >      sprintf( painCave.errMsg,
91 >               "neither --sele1 option nor $SELECTION1 is set");
92 >      painCave.severity = OPENMD_ERROR;
93 >      painCave.isFatal = 1;
94 >      simError();
95      }
96 +  }
97      
98 <    if (args_info.sele2_given) {
99 <        sele2 = args_info.sele2_arg;
100 <    }else {
101 <        char* sele2Env = getenv("OOPSE_SELE2");
102 <        if (sele2Env) {
103 <            sele2 = sele2Env;            
104 <        } else {
105 <            sele2 = sele1;
103 <        }
98 >  if (args_info.sele2_given) {
99 >    sele2 = args_info.sele2_arg;
100 >  }else {
101 >    char* sele2Env = getenv("SELECTION2");
102 >    if (sele2Env) {
103 >      sele2 = sele2Env;            
104 >    } else {
105 >      sele2 = sele1;
106      }
107 +  }
108  
109 <    //parse md file and set up the system
110 <    SimCreator creator;
111 <    SimInfo* info = creator.createSim(mdFileName, false);
109 >  //parse md file and set up the system
110 >  SimCreator creator;
111 >  SimInfo* info = creator.createSim(dumpFileName, false);
112  
113  
114 <    CorrelationFunction* corrFunc;
115 <    if (args_info.dcorr_given){
116 <        corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
117 <    } else if (args_info.rcorr_given) {
118 <        corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
114 >  TimeCorrFunc* corrFunc;
115 >  if (args_info.dcorr_given){
116 >    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
117 >  } else if (args_info.rcorr_given) {
118 >    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
119 >  } else if (args_info.r_rcorr_given) {
120 >    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
121 >  } else if (args_info.thetacorr_given) {
122 >    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
123 >  } else if (args_info.drcorr_given) {
124 >    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
125 >  } else if (args_info.vcorr_given) {
126 >    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
127 >  } else if (args_info.helfandEcorr_given){
128 >    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2);  
129 >  } else if (args_info.lcorr_given) {
130 >    int order;
131 >    if (args_info.order_given)
132 >        order = args_info.order_arg;
133 >    else {
134 >      sprintf( painCave.errMsg,
135 >               "--order must be set if --lcoor is set\n");
136 >      painCave.severity = OPENMD_ERROR;
137 >      painCave.isFatal = 1;
138 >      simError();
139      }
140 <    else if (args_info.vcorr_given) {
141 <        corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
142 <    }
140 >        
141 >    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
142 >  }
143  
144 <    if (args_info.output_given) {
145 <        corrFunc->setOutputName(args_info.output_arg);
146 <    }
144 >  if (args_info.output_given) {
145 >    corrFunc->setOutputName(args_info.output_arg);
146 >  }
147  
148  
149 <    corrFunc->doCorrelate();
149 >  corrFunc->doCorrelate();
150  
151 <    delete corrFunc;    
152 <    delete info;
151 >  delete corrFunc;    
152 >  delete info;
153  
154 <    return 0;  
154 >  return 0;  
155   }
156  
157  

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